Loops were firstly called using the ABC Model. Since this method integrates ATAC-seq, H3K27ac and gene expression data when calling enhancer-promoter (E-P) pairs, we can be more confident we are truly calling loops. After defining E-P loops, differential loop calling was performed using a modified DESeq2 approach via Hictoolsr.
ABC model results
Download Enhancer_promoter_loops.csvDifferential loop analysis
Differential loop analysis was performed at 1000kb resolution (ie. regions were binned at 10kb windows).
Raw counts
Counts
E-P pairs
DESeq2 res
PCA
Top 500 most variable loops
All loops
MA plot
